The Arrest of Commander Shepard
by Sun-Tsu Toriden
Summary: "When Earth calls, you better be ready to face the music with your dress blues on" The time has come for Illyria Shepard to begin to face the consequences of her actions. UPDATED: Now with a follow-up of her house arrest in Vancouver.
1. Chapter 1

"When Earth calls, you better be ready to face the music with your dress blues on."

Those were the parting words of Admiral Steven Hackett as he left the _Normandy_. It had been a month since then, and almost all of Shepard's crew had gone their own ways to prepare for the coming invasion. Just after they had left Illium dropping off the last of those who wished to leave, there came the call.

Hackett had contacted the Normandy on a priority channel, which Illyria took in the conference room. She saluted as the holographic Admiral materialised on top of the table. He looked stressed, the scar on his cheek a little more visible and a definite strain in his eyes.

"At ease Shepard," he said, returning the salute and letting Shepard come to a parade rest stance. "I only wish this call was under friendlier circumstances."

"I understand sir. Can I assume the trumpets are playing for me?"

"Correct. Effective immediately, there is an arrest warrant for you and the _Normandy_. You are being charged with numerous offences. I'm aware you could invoke Spectre authority to deny this warrant, if you wish. Is this your intention?"

"No Sir. It's time I came home."

Illyria couldn't never be sure, and if she was right she'd take it to her grave, but just for a moment Hackett seemed to relax. He'd obviously been thinking about it and the difficulty her Spectre status could be. The thought had crossed her mind as well, but she needed to be back in the Alliance and their sphere of influence if she was going to make any real difference to what was coming. You had to take the good with the bad though, and that meant being arrested.

"Understood Commander," Hackett replied, the first time he had referred to her by rank since she'd woken up nearly a year ago. "Since we have no Jurisdiction outside Council space, I'm offering you the choice of location for your surrender."

"Acknowledged Sir. What will become of the Normandy and the crew remaining aboard?"

"Your ship will be impounded and studied. The Alliance will want to know how Cerberus managed to make a copy of one of the most advanced and classified prototypes to date. As for the crew, they will likely be held and interrogated, and possibly charged with separate offences or as accessories to your own charges."

"If I asked for their immunity as part of my negotiated surrender, would it be accepted?"

"No Commander, I'm sorry, but my hands are tied in this matter. These orders come straight down from the Fleet Master and Parliament. Anyone on board your ship during your surrender will be tarred with the same brush you will be. I've fought them as long as I could Shepard, and got them to back down on a few points, but this is the only deal you are going to get. If you don't take it, I have orders to mobilise the entire Fifth Fleet to hunt you down. I'd rather not have to do that Commander."

Illyria stood still for a moment, pondering her options. There weren't many. She would try and have the few that remained launched out of lifepods before the rendezvous point, but it would probably do little. She wanted to shield the crew from the repercussions, from the fallout of actions that were hers and hers alone, but that wasn't going to be the case this time. Just working for Cerberus was enough to make them suspicious to Alliance investigators. This time, they'd have to accept the consequences of that action, even if it did have the best intention.

She looked back up at the Admiral, still standing in the hologram, patiently waiting for her answer.

"Very well Admiral. I will surrender the _Normandy_ and myself over Eden Prime in 24 hours. Is this acceptable?"

"Yes Commander. Are there any other questions?"

"What will happen to me after I surrender?"

"You'll be taken to Arcturus first to be processed and arraigned. I imagine there will be a number of interrogations, though you'll have a JAG officer assigned to you to protect your legal rights. After that, you'll probably be remanded in custody until a military tribunal can be called. I can't tell you where, but it will be planet-side at an Alliance base. I can't say more than that Commander."

"Understood Admiral. I'll see you in 24 hours."

"Acknowledged. Hackett out," replied the old Admiral, cutting the transmission.

Illyria walked out to the CIC and the galaxy map, staring at it for a while, watching the serene dance of the celestial arms. She worried about the four that had chosen to stay behind, those that had chosen loyalty to Shepard. They still had a chance to leave on Illium and make their own way, and Shepard was going to give them that chance. She tapped the intercom button.

"Attention everyone. In 24 hours, I intend to surrender the _Normandy_ and myself to the Alliance. I've been informed that any and all who are still aboard at that time will be similarly arrested and the Normandy impounded. If you wish to leave the ship and avoid this, now is the time." She waited for the four of them remaining to respond.

"I'm not going anywhere," came the thick Scottish accent of Donnelly. "I'm proud of what we did, and I'm proud to have served with you Commander. If they want to try and make that a badge of shame rather than honour, I'll still wear it proudly right up to the point they put me against the wall and fire. I'm with you Commander, till the end."

"Me as well Commander," piped in Daniels.

"I've had a long life, and a longer career Shepard," came the low measured voice of the doctor. "They can't take that away from me, and you'd be surprised at just how ineffectual any threat they make against me might prove."

"I physically cannot leave the ship, but if I could, I still would remain Shepard," came the synthesised voice of EDI. Shepard smiled as she saw the AI had finally taken her advice and programmed herself a new holographic interface. It was a woman, still detailed in blue light, but she was attractive. Long, wavy hair cascaded down the neck to the edge of the bust, a delicate nose above small but not thin lips, a gently angled jawline and, of course, blue eyes. But it was the larger significance, her first steps into a brave new world, that made Shepard smile.

"Thankyou EDI."

Silence reigned for a while, with no response from Joker.

"Joker, what about you?" Still nothing. Illyria jogged up the helm, wondering if his remarks were too personal to be said over the intercom. She found him with his chair turned around, struggling to stand. Depsite robotic bracers and a few medical implants of his, standing was still a challenge for him. She reached him just as he straightened his spine. He looked up to see her standing before him, and he did something that she never would have thought possible.

He stood straight, tall and proud, and fired off a salute a career drill sergeant would find no fault with. Stunned for a few seconds as he stood frozen, she regained her senses and returned it, allowing him to come to ease.

"You've always done the right thing by me Commander. You stood by me, even though you had every reason not to." They shared a few seconds of silence as they remembered the final moments of the last Normandy. "What kind of subordinate, person and friend would I be if I didn't stand by you when things got tough?" Shepard was amazed. Joker was never one to respect authority, and even less of a one to be serious at all, but this was the first time she'd seen him do it and mean it, _really_ mean it. That alone meant more than could ever truly be spoken aloud. She extended her hand to shake his, which he did.

"It's been an honour Flight Lieutenant. Ready for one last adventure together then?"

"Just say the word."

"Alright, set a course for Eden Prime."

"Aye Aye."

* * *

Later, as the Normandy was in orbit of Eden Prime, the five humans were found in the lounge, enjoying a drink and telling tales of happier times and adventurous exploits. They were only interrupted in their fun when EDI's avatar appeared hear the bar.

"Commander, I have a small flotilla on an intercept trajectory, and actively hailing the ship. The flagship appears to be the _Orizaba_. In addition, there are several cruisers and frigates, including one that bears a similarity to the original _Normandy_."

"Admiral Hackett's welcoming committee no doubt. Alright, finish your drink and then let's all go and get arrested, shall we?" Illyria said, before draining her glass and standing up. The others quickly followed suit, Chakwas helping an indignant Joker to his feet and to the elevator. The five of them stood at the airlock, just as EDI opened a channel to a frigate coming up alongside them.

"Independent ship _Normandy_, this is the Alliance Frigate SSV _Gallipoli_. Prepare to be boarded."

"Acknowledged _Gallipoli_. _Normandy_ stands ready to receive," replied Shepard. A few seconds later there was a thump as the docking hatch locked, followed by the hum of the decon chamber and then finally the airlock opened to reveal the boarding party. Admiral Hackett himself stood at the head, accompanied by a mountain of a man with lieutenant markings on his shoulder. Behind them, a dozen armed and armoured MPs stood ready.

"Commander Shepard, you are hearby charged with offences against the Alliance and the galaxy. Are you going to surrender?" asked Hackett. Everyone knew it was merely a formality at this point, but the fact the Hackett himself was doing it and not some faceless MP Colonel meant a lot to Illyria.

"I surrender myself, my crew and my ship to your custody Admiral."

"Lieutenant Vega, please escort Commander Shepard to the _Gallipoli_ to await transfer to the _Orizaba_." The man mountain moved towards Illyria and held out a pair of flex-cuffs. She obediently held out her own hands while Vega attached the cuffs. Hackett then pointed to Chakwas, Donnelly and Daniels. "Take these three to the SSV _Canberra_." He looked at Joker last. "You two, allow the pilot to manoeuvre the Normandy to the docking cradle on the _Orizaba_ for transport. After docking, transfer him to the SSV _New York_."

As the orders were carried out and the crew of the Normandy was split up between the various ships, Illyria felt a sense of sadness. The first time she had been forced to let the _Normandy_ go, it was fatal. This time wasn't, but it made her think about how David Anderson had felt when he had been forced to leave the _Normandy_. At least the Admiral had given her the personal consideration of letting her end it on her own terms, rather than anyone else's. Now all she had to do was get someone to listen to her and prepare for the coming war.


	2. Chapter 2

**THREE MONTHS LATER**

The door to Shepard's cell opened and the ever-present Lieutenant James Vega walked in. Well, calling it a cell was misleading. It was in fact a small apartment with a single small bedroom, a bathroom and a kitchenette; and Illyria had even been allowed to give it a few personal touches. But there remained the fact they had confiscated her omni-tool, there was no terminal to access even the most basic extranet sites and the only real entertainment she had was a single datapad hard-linked to a standalone server of reading material and vids. She was allowed to cook her own food, though not pick her own ingredients. She was allowed visitors, though the only ones she really got were James, the odd Admiral and her JAG officer, an intelligent Canadian major by the name of Cassandra Selene. Make no mistake; she was still a prisoner, just with a nicer cell.

He walked over to the former Commander having breakfast and saluted. "Good morning Commander."She waved at him dismissively with her spoon, and he dropped the salute.  
"Not supposed to call me that anymore James. Or salute for that matter. I'm a civvie now!" she said with feigned enthusiasm.  
"Well, you know what they say, old habit die hard and all that."  
"Fair enough James. So, what's my schedule for today? Anyone want to come and see how far the mighty have fallen? Want to lean down and spit on me? Call me a traitor or worse, call me a hero?" she put her spoon down and pushed away the bowl, suddenly no longer hungry. She really hated her confinement some days. It gave her too much time to think, and not enough topics to think about to stop her making herself out to be the lowest form of trash in Vancouver.

"Don't know about any of that, but you do have an Admiral coming to visit. Something about mail." Illyria perked up at the mention of mail. She'd had nothing, no email, no calls, not even an acknowledgement that any and all incoming correspondence was being halted.  
"What's this about mail?"  
"I wasn't told details; just that someone was coming in about an hour." Illyria deflated a little, and tried not to get her hopes up.  
"So, am I allowed to go for a walk today James, or am I still under house arrest?"

"You know the rules ma'am." Shepard flinched at being called ma'am. She'd always been called by her rank or name for as long as she could remember, but never ma'am. "You're allowed free use of the facilities on this floor, and the pool and gym downstairs, as long as you're escorted. If it were up to me, I'd allow you to take a walk down in the park there was well, but I guess they think you're a flight risk, considering." Illyria sighed, if she was going to arrange something like this for a prisoner like her, she'd probably do much the same.  
"Can't say I blame them James. I just wish I could keep my amp. I feel slow and heavy without being able to use my biotics. Plus there's nothing quite like the feeling of a charge."  
"I'll have to take your word on that. I prefer a good set of iron myself." A statement backed up by the sheer size of his arms and chest. _Though he still needed to work a bit on his legs_, thought Shepard, _their build for strength, but not stamina_. _He's never going to make it passed the basic A rating without it. _

Too much time had given her time to scrutinise James Vega. She couldn't access his file, but she could read a pair of dog tags like anyone else. He was a B7, highest specialisation level for a pure soldier, but she suspected that he'd probably make at least N3 without trouble. Though without working on his stamina, particularly in his legs, he'd never get any further. N7s were the best for a reason, and it wasn't just about brute strength. Thankfully, she could keep up with her physical training while she was in custody here, but she knew her biotics would suffer if she ever got the use of her amp back.

She eventually decided on some laps in the pool while Vega looked on, the two of them trading the occasional story as she notched up the lengths. When she was done, they both retired to her residence and waited for the Admiral to arrive. They were in the middle of Shepard showing Vega her poker skills when the door opened and the Admiral arrived. Correction, two Admirals. She failed to fight the impulse to jump up and salute as the Admirals entered, in perfect sync with Vega. Admirals Donesh and Anderson saluted in return.

"At ease," said Donesh. A capable woman of German decent, there were still hints of her original blonde hair interspersed through her silver. She was not unkind to Shepard, though she had been a close friend of Admiral Kahoku and didn't miss an opportunity to remind Shepard when she came. She'd been heavily involved in her debriefing, along with Hackett and eventually Anderson. Shepard was shocked when her old friend and CO had arrived in the room with the other admirals, sporting the four gold bars himself, and when asked he simply said that he had resigned the Councillor position and been offered the position by the Alliance.

"Admirals, was there something particular we need to discuss?" asked Illyria calmly. Anderson and Donesh shared a look.  
"Yes, but first a question Shepard. Have you been in contact with anyone since you've been arrested?" Shepard wondered why they were leading with a question like that, and decided to pry as best she could.  
"Admirals, I've been monitored for electronics since the moment I stepped off the _Normandy_. I receive no mail or other correspondence, I suspect because it's all blocked by the Alliance. The only people I see here are Vega, my JAG officer and a few Admirals. I'd bet money on the fact that Vega is searched every day to make sure I can't get anything out and even the most bent JAG would resign rather than do something as outright illegal as that. I don't have the technical skills to unlock the datapad you so generously granted me. So no, I haven't been in contact with anyone. Why do you ask?" If Donesh had been affronted by Shepard's tone or words, she gave no outward sign of it. Anderson leaned forward and muttered something in Donesh's ear and Illyria though it sounded like _I told you so_.

"I'm asking Commander, because despite all the measures we have put in place for your own security, there has been a package laid at our doorstep that is different from the others." She took a step inside and looked out the window to the park across the street. "Do you have any idea how many credible death threats you've received since your arrest?"  
"Not a clue."  
"Twenty-six," Donesh replied. "Ten of them were actual bombs. A lot of people want you dead Commander. But yesterday, we received something else entirely." The older woman turned back to Illyria. She nodded towards Anderson, who brought out a black box from behind his back. "Yesterday, one of the known agents of the Shadow Broker delivered this to Arcturus, with strict instructions it be delivered to you." Illyria tried not to be too interested. She was one of the few people in the galaxy who knew the true identity of the Shadow Broker, and probably the only one who knew her as Liara T'Soni, her lover. "Of course I tried to block it, but several calls from key figures in the Alliance military and Parliament overruled it and insisted it be delivered. I for one was against it until we knew what was inside it. Given the bombs we'd already intercepted, I thought it only prudent."

Donesh stepped closer to Illyria, a penetrating stare on her face. "So imagine my surprise when all attempts to scan this piece turned up nothing. And when we tried to open it physically, a not warning sounded that anyone other than Illyria Shepard trying to open the box would be electrically shocked to discourage them." Donesh looked over at the box again. "Apparently, whatever is in the box the Shadow Broker thinks is for your eyes only, and I'm getting sick of all the calls from everywhere insisting I give in the Broker's demands." She gave a hard look at Anderson, whose only reply was to give Shepard a small smirk when Donesh stopped looking at him.

"So fine then. If you want to die so badly, then I say why not. But just remember this Shepard. Not all of the Admirals here are against you. I could have let any of those bombs through if I wanted you dead. I'm not doing this to be vindictive or spiteful; I'm just doing my job." With that she walked out, before Shepard could say anything. Anderson gave her a sad smile as he placed the box on the small bench that was the only table space in the place.  
"I'm sorry it had to come to this Shepard. If it had been me, I'd have let through more of your mail, but that's not up to me." He placed a fatherly hand on her shoulder. "I'm still trying to fight for you, so don't think I've given up either." Illyria placed her hand over his. "Thank you David. You're a good friend, and I'm glad to have you. I just wish I had more like you."  
"Don't we all," he said wearily, before saying his goodbyes and leaving her.

Vega and Shepard, alone now, looked at the box.  
"So, you gonna open it?" he asked slowly.  
"When you leave, sure. I'm pretty sure it's my eyes only."  
"Ok, I can take a hint. So I'll see you tomorrow then, no?"  
"Same time, same place I'm sure," replied Illyria. She just wanted privacy, and wondered what it was that Liara had gone to such lengths to deliver to her.

She stroked the top of the box, looking for a lid or flap to lift up. Instead a little electronic voice piped up.  
"Genetic match confirmed Commander Shepard. Releasing locks." As the voice stated there was the sound of magnetic locks opening, and the top of the box opened outwards to display everything inside it. There were numerous smaller packages all wrapped in black velvet, and on top of it all was a small OSD. She picked up the disk first, inserting it into the datapad. Almost immediately, the screen was filled with a beautiful blue face that Illyria had been missing for three months.

"Hello Illyria. I'm sorry to have to resort to this, and I hope it doesn't get you into too much trouble. I've been sending you messages and trying to call, but the Alliance has blocked all communication to you, so I had to flex a bit of muscle to get this too you. Nothing to major, some blackmail here, a few threats there." There was a pause and she looked down at what Shepard assumed was her hands. "I love you Illyria, never doubt that for one second. I would be with you right now if I could, but we both know that wouldn't be the best use of my time right now. Another reason I got this to you is to tell you that I'm alright, and I've been offered an archaeology job. I'm sorry I can't tell you the details, but it's being sponsored by the Alliance.

Anyway, about this package. I know for a fact that you didn't have much in the way of personal effects when you surrendered the _Normandy_, and I recovered a few things they were attempting to throw away during the refit. Oh, I guess you probably didn't know about that. The Alliance is refitting the _Normandy_ in the place called... Canada? I don't know where that is in relation to you, but I hope it gives you some peace. Anyway, these things are mostly sentimental, though I hope you'll be very... satisfied with some of the new items I included." Illyria couldn't help but smile as she was the devious imp grin on Liara's face. She'd come so far from the shy, quiet archaeologist she'd rescued on Therum three years ago.

I know we can't be together right now Shepard, and we might not be for some time yet, but I will always be with you Shepard. Be well, and enjoy these few gifts I can give you until I can hold you again in my arms." With that the OSD ejected from the datapad and began to smoke. _Of course_, thought Illyria, _no evidence_. She threw it into the recycler and then focused on the items in the box.

The first one she pulled out felt like a frame, and as she unwrapped it she found her original dog tags, the ones Liara had recovered from her body before giving it to Cerberus. She held back a tear from remembering when Liara had given them to her after becoming the Broker, and went and set it reverentially by the bed. The next item did make her cry. It was a framed picture of Shepard and Liara just after the Battle of the Citadel. Illyria's arm was still in a sling, and Liara sported a bandage on her forehead from a cut, but the two of them were smiling like all their birthdays had come at once. It then changed to another one taken seconds later, the two of them sharing a tender and loving kiss, before going back to the kiss. Illyria put this one next to the dog tags and then took out the final two pieces inside. The third piece, largest and heaviest one, turned out to be a model kit for a ship, the Normandy that had been built by Cerberus, though this time painted entirely black with a familiar red and white stripe down the centre. She smiled as she put it on the bench to assemble later, and took the last piece out of the box.

Her embarrassed smile and blush revealed that Liara had indeed been thinking about her well-being. Well, one particular aspect at any rate. The contents of the last package were something that she had once discussed with Liara, and they had both enjoyed the topic of that discussion. Liara had even included a hand-written note in case she'd forgotten. Inside the black wrapping Shepard had discovered a copy of the only adult vid that Shepard had felt brave enough to share with Liara in the initial stages of their relationship after the Battle of the Citadel.

Illyria recalled sheepishly saying she'd watched part of it to learn what asari found sexually appealing. Liara had blushed at seeing it was a softer vid that showed an asari and a human female, and some sort of discussion about paying for pizza delivery. They had both watched it, first with horrified fascination and then with genuine curiosity. After watching they tried to apply what they'd learned from the vid on each other, and both were surprised at how much better they were for each other because of it.

The second part of the package turned out to be a vibrator, blue and textured to feel like asari skin, and that used not only a conventional motor but also micro-mass effect fields to enhance the experience. Shepard stared at it in fascination for several long, pregnant moments.

* * *

Hours later, Shepard had to admit that while it wasn't nearly as good as it had been, the two of their warm naked bodies seeming to float with their biotics and their minds adrift in the meld, the particular vibrator Liara sent her would do for now.


End file.
